Remote access to crystallography beamlines at SSRL: novel tools

electronic reprintJournal of

AppliedCrystallography

ISSN 0021-8898

Editor: Anke R. Kaysser-Pyzalla

Remote access to crystallography beamlines at SSRL: noveltools for training, education and collaboration

Clyde A. Smith, Graeme L. Card, Aina E. Cohen, Tzanko I. Doukov,Thomas Eriksson, Ana M. Gonzalez, Scott E. McPhillips, Pete W. Dunten,Irimpan I. Mathews, Jinhu Song and S. Michael Soltis

J. Appl. Cryst. (2010). 43, 1261–1270

Copyright c© International Union of Crystallography

Author(s) of this paper may load this reprint on their own web site or institutional repository provided thatthis cover page is retained. Republication of this article or its storage in electronic databases other than asspecified above is not permitted without prior permission in writing from the IUCr.

For further information see http://journals.iucr.org/services/authorrights.html

Many research topics in condensed matter research, materials science and the life sci-ences make use of crystallographic methods to study crystalline and non-crystalline mat-ter with neutrons, X-rays and electrons. Articles published in the Journal of Applied Crys-tallography focus on these methods and their use in identifying structural and diffusion-controlled phase transformations, structure–property relationships, structural changes ofdefects, interfaces and surfaces, etc. Developments of instrumentation and crystallo-graphic apparatus, theory and interpretation, numerical analysis and other related sub-jects are also covered. The journal is the primary place where crystallographic computerprogram information is published.

Crystallography Journals Online is available from journals.iucr.org

J. Appl. Cryst. (2010). 43, 1261–1270 Clyde A. Smith et al. · Remote access to SSRL beamlines

http://journals.iucr.org/j/

http://dx.doi.org/10.1107/S0021889810024696

http://journals.iucr.org/services/authorrights.html

http://journals.iucr.org/j/

http://journals.iucr.org

teaching and education

J. Appl. Cryst. (2010). 43, 1261–1270 doi:10.1107/S0021889810024696 1261

Journal of

AppliedCrystallography

ISSN 0021-8898

Received 4 February 2010

Accepted 23 June 2010

# 2010 International Union of Crystallography

Printed in Singapore – all rights reserved

Remote access to crystallography beamlines atSSRL: novel tools for training, education andcollaboration

Clyde A. Smith,* Graeme L. Card, Aina E. Cohen, Tzanko I. Doukov, Thomas

Eriksson, Ana M. Gonzalez, Scott E. McPhillips, Pete W. Dunten, Irimpan I.

Mathews, Jinhu Song and S. Michael Soltis

Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA. Correspondence e-mail:

[email protected]

For the past five years, the Structural Molecular Biology group at the Stanford

Synchrotron Radiation Lightsource (SSRL) has provided general users of the

facility with fully remote access to the macromolecular crystallography

beamlines. This was made possible by implementing fully automated beamlines

with a flexible control system and an intuitive user interface, and by the

development of the robust and efficient Stanford automated mounting robotic

sample-changing system. The ability to control a synchrotron beamline remotely

from the comfort of the home laboratory has set a new paradigm for the

collection of high-quality X-ray diffraction data and has fostered new

collaborative research, whereby a number of remote users from different

institutions can be connected at the same time to the SSRL beamlines. The use

of remote access has revolutionized the way in which scientists interact with

synchrotron beamlines and collect diffraction data, and has also triggered a shift

in the way crystallography students are introduced to synchrotron data

collection and trained in the best methods for collecting high-quality data.

SSRL provides expert crystallographic and engineering staff, state-of-the-art

crystallography beamlines, and a number of accessible tools to facilitate data

collection and in-house remote training, and encourages the use of these

facilities for education, training, outreach and collaborative research.

1. Introduction

The macromolecular crystallography (MX) experiment lends

itself perfectly to high-throughput technologies, automation

and remote experimentation. The experiment comprises a

series of distinct steps, beginning in the wet laboratory with

protein expression, purification, crystallization and crystal

mounting using flash-cooling in liquid nitrogen, and progres-

sing through to the screening of crystals for diffraction quality,

the collection of diffraction data, data processing and struc-

ture determination. Most of these steps have been fully

automated, and in many cases it is now possible to go from

expressed protein to fully determined three-dimensional

structure with only minimal intervention. However, several

steps still require expert human intervention, including the

choice of crystal for data collection. Since the ultimate goal of

the experiment is to produce a high-quality high-resolution

structure of the protein in question, this relies heavily upon

the choice of the best possible crystal for data collection and

the most appropriate data-collection strategy. In this regard,

the careful training and education of students and novices is of

fundamental importance to these aspects of the process and

cannot be overlooked, however much automation and remote

access are involved in the experiment.

Some of the most important developments in the automa-

tion of protein expression, purification and crystallization

have taken place under the auspices of the NIH-funded

Protein Structure Initiative (Burley et al., 2008). With regard

to high-throughput crystal screening and data collection, many

facilities and groups worldwide have developed automated

sample changers, including Abbot Laboratories in Illinois,

USA (Muchmore et al., 2000), DORIS in Hamburg, Germany

(Karain et al., 2002; Pohl et al., 2004), the Spring8 synchrotron

in Japan (Ueno et al., 2004), the European Synchrotron

Radiation Facility in Grenoble, France (Ohana et al., 2004;

Cipriani et al., 2006) and the Advanced Light Source (ALS) in

Berkeley, California, USA (Snell et al., 2004). In an effort to

produce a true high-throughput crystal-screening and data-

collection facility, and to improve the efficiency of the

synchrotron radiation resource, the Stanford Synchrotron

Radiation Lightsource (SSRL) Structural Molecular Biology

(SMB) Group and the Structure Determination Core of the

Joint Center for Structural Genomics (JCSG) (Lesley et al.,

2002) worked together to develop the Stanford auto-mounting

electronic reprint

(SAM) system (Cohen et al., 2002). In addition to complete

automation of the experiment, SSRL has also implemented

fully remote access to the MX beamlines (Soltis et al., 2008).

Notwithstanding the obvious increase in throughput and

efficiency, the advent of automation and remote access at the

SSRL MX beamlines has generated substantial spinoffs for

the scientific user community by providing increased oppor-

tunities for collaboration between research groups and

allowing scientists who might not typically have had access to a

national user facility to obtain valuable beam time. It has also

introduced many young scientists to synchrotron radiation

science by providing educational and training opportunities

for graduate students and postdoctoral researchers in user

laboratories. The scientific staff at SSRL offer in-house

training workshops and have run remote-access workshops

around the US and at international sites. Attending one of

these workshops is strongly encouraged before taking part in

remote-access beamtime. Furthermore, often the most effec-

tive training is from the experiences gained during remote-

access beamtime, when new researchers conduct their own

experiments under the advice and encouragement of other

members of the home laboratory and of SSRL User Support

scientists, who are readily available via cellular telephone,

email and a ‘chat’ feature (instant messaging) in the BLU-

ICE/DCS beamline control system.

2. Synchrotron radiation research at SSRL

SSRL has a long history of excellence in structural biology

research, including some of the first reports of X-ray absorp-

tion spectra from a biological sample (Kincaid et al., 1975), the

first published report of single-crystal diffraction from protein

crystals using synchrotron radiation (Phillips et al., 1976),

fundamental studies of what would become the multiple-

wavelength anomalous diffraction phasing experiment (Phil-

lips et al., 1977, 1978; Phillips & Hodgson, 1980; Templeton et

al., 1980) and the development of insertion devices as sources

of high-intensity radiation (Doniach et al., 1997).

SSRL is a national user facility funded by the US Depart-

ment of Energy Office of Basic Energy Science, the National

Institutes of General Medical Sciences (NIGMS) and the

National Center for Research Resources, the latter two being

components of the US National Institutes of Health (NIH).

SSRL provides extremely bright X-ray and UV photon beams

produced by the third-generation 3 GeV SPEAR3 storage

ring, for applications in materials science, environmental

science, chemistry and structural biology research, utilizing

scientific techniques including photoelectron spectroscopy,

small-angle X-ray scattering (SAXS), X-ray absorption spec-

troscopy (XAS), total X-ray reflection fluorescence and MX.

The SMB group at SSRL (http://smb.slac.stanford.edu)

operates and maintains ten beamlines, seven for MX (BL1-5,

BL7-1, BL9-1, BL9-2, BL11-1, BL12-2 and BL14-1), two for

biological XAS (BL7-3 and BL9-3) and one for biological

SAXS (BL4-2). All seven MX beamlines at SSRL are fully

automated, employing the SAM system which has been inte-

grated into the BLU-ICE/DCS beamline control system and

graphical user interface developed earlier at SSRL (McPhil-

lips et al., 2002). Up to 288 crystals can be screened in a matter

of hours without manual intervention using this reliable and

robust robotic system. The use of the SAM system has not

only seen an increase in throughput by research groups but

also an improvement in the overall quality of the diffraction

data being collected. Researchers are now able to screen all

their crystals reliably and take advantage of the automated

image-analysis tools developed at SSRL, prior to choosing the

best quality crystals for subsequent diffraction data collection.

These tools include the Crystal Analysis server, which will

automatically analyze test images and feed relevant para-

meters and statistics back to the researcher via BLU-ICE, and

the browser-based WEB-ICE interface (Gonzalez et al., 2008),

where diffraction and video images of the samples can be

viewed, crystals ranked and data-collection strategies calcu-

lated.

2.1. Automation

The seven SSRL MX beamlines are all very similar, in that

the experimental table, front-end beam-conditioning system,

kappa goniometer, cryosystem and detector positioner are

nearly all identical. The undulator micro-focus beamline

(BL12-2) differs somewhat in design to meet the more

demanding hardware requirements for microbeam and

microcrystal experiments, but is still compatible with the SAM

system and standard beamline control software. Every aspect

of beamline control inside the experimental hutch, and also on

the upstream optics elements (mirrors, monochromators and

slits), is motorized to the extent that it is unnecessary to enter

the hutch to change any of the experimental parameters

(X-ray energy, beam size, X-ray detector position, fluores-

cence detector position, beamstop position, attenuation and

lighting), to mount or dismount samples, or to anneal or wash

ice from samples. This degree of automation of the beamlines

is absolutely critical to the implementation of fully remote

access; if there remains a single task that requires human

intervention inside the hutch during the normal course of

crystal screening and data collection then remote access is not

practical.

Automated sample mounting was made available to general

experimenters during the first SPEAR3 run of 2004 on three

beamlines. Since its inception, use of the SAM system has

accelerated such that, during the last scheduling period (2009),

110 out of 121 research groups (91%) were using SAM during

their experiments. The SAM system has been described in

detail previously (Cohen et al., 2002; Smith & Cohen, 2008;

Soltis et al., 2008). During the first year of operation (2004), 30

research groups used the automated mounter and over the

course of 60 experimental starts mounted over 3500 crystals.

The JCSG, one of the original SAM test user groups, mounted

an additional 2000 or more crystals from 125 target proteins

that year, and were successful in solving 30 new structures

from 36 unique proteins (Smith & Cohen, 2008). The number

of crystals mounted using the SAM system has also increased

dramatically since it was first introduced, such that currently


1262 Clyde A. Smith et al. � Remote access to SSRL beamlines J. Appl. Cryst. (2010). 43, 1261–1270

electronic reprint

well over 300 000 crystals have been screened by researchers

(Fig. 1).

2.2. The remote-access experiment

Fully remote access was made available to research groups

during the 2005 scheduling period. During the first two years

the number of research groups choosing to conduct their

experiments remotely rose from 24 to 44%, and has continued

rising each year (Fig. 2a) until the last scheduling period,

which saw 105 of the 121 groups (87%) screening their crystals

and collecting their data using remote-access tools. Most

noticeably, the total number of remote starts saw an almost

exponential growth in 2007 (Fig. 2b), which can be primarily

attributed to an increase in beamline efficiency (fewer beam-

hours per start) as the coupled use of the SAM system and

remote access became more popular. This increase in beam-

line efficiency can also be seen in the total number of crystals

mounted via the SAM system since its inception, which also

experienced a dramatic rise in 2007 (Fig. 1).

The remote-access experiment at SSRL has been described

previously (Smith & Cohen, 2008; Soltis et al., 2008). Scientists

ship their cryo-cooled samples to SSRL in 96-port cassettes

custom-designed at SSRL for use with the SAM system, or in

16-port Uni-pucks (http://smb.slac.stanford.edu/robosync/

Universal_Puck). The cassettes have been designed such that

two can be shipped in a standard dry shipper (192 crystals in

total). Up to seven Uni-pucks (112 crystals in total) may be

shipped in a standard dry shipper. The Uni-pucks have been

designed as part of a collaboration between developers at

synchrotrons throughout the United States, allowing research

groups to take advantage of automated sample-mounting

systems at different synchrotron facilities (http://smb.slac.

stanford.edu/robosync/). The Uni-pucks are based upon the

ALS-style puck, and are currently used with the SAM robot at

SSRL, with many ALS-style robots at the three other large

DOE-funded synchrotrons in the US (ALS, the Advanced

Photon Source and the National Synchrotron Light Source),

with the ACTOR robot (Rigaku, USA), and with various

other sample-mounting robots in Europe, Australia and Asia.

At SSRL, four Uni-pucks are mounted in an adaptor cassette

such that the sample pins can be accessed by the SAM system

in the same way as it accesses sample pins in an SSRL cassette.

During their allotted beam time, the remote researchers

connect to the beamline computers via an NX server/client

application (http://www.nomachine.com). The NX client is

downloaded for free onto the researchers’ home computers,

and they can then connect to an NX server running on an

SSRL computer. The client uses minimal CPU and memory

resources on the host computer, with the entire computational

load on the SSRL server. Once connected, the researchers see

a remote desktop (Fig. 3a), identical in all aspects to the

environment they would see on a computer at the beamline.

They can then use the BLU-ICE control interface (McPhillips

et al., 2002) and/or the WEB-ICE interface (Gonzalez et al.,

2008) to screen their crystals and obtain results directly back

into the BLU-ICE screening interface (Fig. 3b), collect


J. Appl. Cryst. (2010). 43, 1261–1270 Clyde A. Smith et al. � Remote access to SSRL beamlines 1263

Figure 1Total number of samples mounted each year with the SAM system sinceits release in 2003. To date, over 300 000 samples have been screened bymore than 100 research groups.

Figure 2(a) The total number of groups with active proposals at SSRL (blue bars)and the number of research groups using remote access since its release in2005 (purple bars). (b) The total number of remote starts (user groupsstarting a remote data-collection run) since 2005.

electronic reprint

monochromatic diffraction data, measure absorption edges

prior to multiple- (MAD) or single-wavelength anomalous

diffraction (SAD) data collection, monitor all aspects of the

experiment, and connect to User Support staff and colla-

borators via a real-time chat feature. In fact, everything that a

crystallographer would typically do during a synchrotron data-

collection visit can be achieved in the

remote-access experiment.

The remote desktop also gives

researchers access to all the crystal-

lographic software installed on the

SSRL computers, for data processing,

structure solution and analysis.

Although experimental control, deci-

sion making and strategy calculation are

carried out in the home laboratory by

the researchers and their students,

research associates, postdoctoral

fellows and/or collaborators (Soltis et

al., 2008), SSRL User Support staff are

available to troubleshoot experiments,

help analyze the screened crystals or

advise on data-collection strategy if

required. This contrasts with the

options that other synchrotrons offer,

known as ‘service’, ‘mail-in’ or ‘FedEx’

crystallography, whereby researchers

send their cryo-cooled samples to the

synchrotron but the decision making

and data collection are carried out

solely by beamline staff (Robinson et

al., 2006), or the more limited tele-

presence described for a small-molecule

crystallography beamline at Daresbury

(Warren et al., 2008).

3. Training and collaboration

Based upon feedback from recent

SSRL remote-access workshops,

remote-access demonstrations at

national and international meetings and

conferences, anecdotal evidence from

informal discussions with research

groups, and a recent remote-access

survey sent to research groups who

regularly use SSRL, the remote-access

capabilities have not only revolutio-

nized the way in which diffraction data

at synchrotrons are collected but also

changed the way in which graduate

students and postdoctoral researchers,

new to crystallography or synchrotron

data collection, are introduced to the

area and trained. The general consensus

is that the remote-access capabilities at

SSRL are a useful tool in training

graduate students and postdoctoral

fellows in the collection of good quality

diffraction data.



Figure 3(a) Screen capture of a typical remote-access NX session showing multiple windows open, includingBLU-ICE in the top left background, the MOSFLM graphical user interface on the bottom right,COOT (Emsley & Cowtan, 2004) at the top right and a WEB-ICE session in the left foreground. (b)Screen capture of the Screening tab from the BLU-ICE software. The spreadsheet at the top left hasbeen loaded by the experimenter, and during initial screening the Crystal Analysis server updatesthe table with results, as shown.

electronic reprint

Prior to automation and remote access, a research group

comprising, on average, three laboratory members (perhaps

one or two experienced people and some graduate students)

would undertake a synchrotron data-collection trip and spend

48–72 h continuously screening crystals and collecting

diffraction data. Since the first beamlines were developed and

made available to the general scientific community, a

synchrotron data-collection trip has almost been viewed as a

rite of passage for scientists, young postdoctoral fellows and

graduate students. It is quite likely that most, if not all,

synchrotron beamline users can remember the first time they

set foot in one of these laboratories. In recent years, with the

increased pressure on funding, the use of research grants to

take a large group of scientists to a synchrotron beamline has

become uneconomical, particularly given the trend towards

increased numbers of crystals being produced in some

laboratories, which necessitates more and more access to

beamlines. Although the use of a national user facility such as

SSRL has no direct cost associated with it (it is mandated that

such facilities give free access to US and international scien-

tists at academic institutions), there are still significant costs

involved with travel and accommodation (Table 1). With the

advent of remote-access data collection, new students or other

laboratory members who would not normally be sent on a

data-collection trip are now exposed to the synchrotron

resource, and this access provides valuable experience for

their future careers in science.

Fatigue from travel and prolonged presence at the beamline

form a hurdle which has, on occasion, given rise to errors and

mistakes during mounting of the crystals, analysis of the

diffraction or determination of the optimum collection

strategy. Prior to the incorporation of the robotic sample

mounter, the screening of flash-cooled crystals typically

involved manual mounting using cryo-tongs pre-cooled in

liquid nitrogen, which enclose the crystal (mounted in a fiber

loop at the end of a sample pin) inside a hollow cavity (Parkin

& Hope, 1998; Rodgers, 2001; Pflugrath, 2004; Smith & Cohen,

2008) to maintain the crystal at cryogenic temperatures during

transfer into the experimental hutch and onto the goniometer.

Although this method has proved to be very reliable since its

inception in the 1990s (Pflugrath, 2004), it becomes laborious

and tedious when repeated many times. The skill and patience

of the experimenter, rather than the number of samples

available, have often dictated the quality of the crystal

selected for data collection; crystals were screened manually

until a crystal deemed ‘good enough’ to collect a complete

diffraction data set was found. In cases like this, other crystals

from the same project would go unscreened; if a better quality

crystal were among those which were unscreened, it would go

undetected and uncollected.

The process of crystal screening, crystal selection and data-

collection strategy determination has become significantly

easier with the implementation of the SAM system, the

Crystal Analysis server and WEB-ICE. As noted above, useful

crystal parameters and statistics [including the Bravais lattice,

the unit-cell parameters, the estimated mosaicity, the

predicted resolution, the r.m.s. fit from MOSFLM (Leslie,

1992) and an overall score] are continually fed back into the

BLU-ICE spreadsheet (Fig. 3b), and these are also accessible

through WEB-ICE, where researchers can also inspect the

diffraction images and crystal video images. The availability of

screening results and the crystal analysis have provided a new

resource for training novice crystallographers during the

experiment. Researchers can easily access and compare

diffraction images, video images of each crystal and the results

of the Crystal Analysis server to decide how best to proceed.

For example, a crystal may need to be rescreened because the

best part of the crystal was not in the beam, or perhaps the

crystal may need washing as it was covered with surface ice

(visible on the crystal images and as strong ice rings on the

diffraction images), or the automated strategy may be

confirmed as a good approach for subsequent data collection.

Access to all this information through WEB-ICE makes it

easier to teach novice crystallographers when to use auto-

mated results and when to question them.

It is undeniable that hands-on experience with the control

systems of a synchrotron beamline, and the ability to analyze

and monitor the data as they come off the detector in real

time, are vital not only to the collection of the best possible

diffraction data (which will ultimately lead to the best possible

structures) but also in the training of the next generation of

synchrotron beamline users. Our contention, which is thor-

oughly backed up by the feedback we have received over the

past five years, is that the training being received by students

and novices via SSRL User Support staff and the SSRL

remote-access tools is fully comparable with the on-site

training they would have received had they made an actual

trip to SSRL or other synchrotron facilities. In most cases this

is a guided participation approach, whereby an experienced

researcher, principal investigator (PI) or SSRL User Support

person will demonstrate the fundamental aspects of the system

to perhaps a small group of students or novice group members,

and then guide them through the experiment as they take

control of the BLU-ICE or WEB-ICE interface. It is well



Table 1Cost comparison between a visit to SSRL and remote-access datacollection.

Costs are in US dollars.

US domestic† International‡ Remote access

Airfares 432.90 1210.00 0Sample shipping 0 0 200§/1000}Meals 191.25 191.25 0Accommodation 195.00 195.00 0Taxes 19.50 19.50 0Rental car 148.00 148.00 0Parking 24.00 0 0Communications†† 0 200.00 20/200

Total per person 1010.65 1763.75 0Total (3 people) 2735.95‡‡ 5195.25‡‡ 220/1200

† Three-day data-collection trip from Huntsville, Alabama, USA. ‡ Three-day data-collection trip from Auckland, New Zealand. § US domestic Dewar shipping by FedExfrom Huntsville. } International Dewar shipping by FedEx from New Zealand.†† Includes telephone calls, internet and ftp data backup. ‡‡ Total includes three timesthe airfare, meals, accommodation and taxes only.

electronic reprint

understood that people learn by different methods, whether it

be through observation, analysis, discussion or activity, or a

combination of these. The remote-access tools available to the

SSRL user groups offer something to all types of learner and

therefore provide a very effective method of teaching the new

user the best possible ways in which to collect the highest

quality diffraction data, this being the ultimate goal of any

X-ray diffraction experiment.

Direct contact with SSRL User Support staff is strongly

emphasized as being the important first step in remote training

for any research group. The User Support staff have a vast

amount of knowledge and expertise with the SSRL beamline

systems, the SAM robot and the remote-access capabilities,

and can direct researchers to the appropriate information and

resources to make their group training, and ultimately their

valuable beam time, a most effective and efficient process.

Moreover, SSRL User Support staff can effectively facilitate

remote training with a research group over the telephone,

employing all the remote-access tools available to the research

group. These tools include (i) access to the SSRL User Guide,

(ii) access to a number of video tutorials which illustrate

various steps in a remote-access data-collection experiment,

(iii) connection to a ‘simulated’ beamline, facilitated through

SSRL User Support staff, (iv) information on software

packages installed and supported on SSRL computers (http://

smb.slac.stanford.edu/public/facilities/software/), (v) access to

test images and data sets so that the processing software and

structure-solution software and scripts can be tested by or

demonstrated to students and novices, (vi) use of the chat

feature in BLU-ICE, and (vii) use of the shared desktop

capabilities of the NX server/client interface, whereby SSRL

support staff can demonstrate the BLU-ICE or WEB-ICE

interfaces while a remote research group follows on their local

computers. The full capabilities of the NX desktop-sharing

tools are described on the developer’s website (http://www.

nomachine.com).

3.1. SSRL User Support

The SSRL User Support staff are a group of expert crys-

tallographers and engineers who are available before, during

and after beam time for consultation and practical help.

Typically, one staff member is responsible for a given beamline

for a specified period, and research groups can determine who

their particular support person will be from the online User

Support schedule (http://smb.slac.stanford.edu/schedule/

sch_staff.cgi). As noted above, research groups are strongly

encouraged to contact the responsible staff member by either

telephone or email prior to upcoming remote-access beam

time to discuss beamline characteristics, sample preparation,

and experimental design and strategy, to gain access to the

simulated beamlines, to test connectivity through the NX

server/client system, and to organize either pre-beam remote

training or training once their beam time starts. The use of

remote training as a teaching tool in research laboratories

assumes the presence in the research group of an experienced

user of the SSRL beamlines and the BLU-ICE or WEB-ICE

interfaces who can facilitate this training. If the research group

is new to SSRL then this may not be the case, and under these

circumstances we strongly recommend that the group send at

least one representative to either an on-site or a remote SSRL

workshop to gain hands-on experience with BLU-ICE and

WEB-ICE, the SSRL computing systems, and in the use of the

cryo-tools associated with the SAM system, the storage and

transport options available, and the proper sample prepara-

tion techniques. Sample preparation is absolutely critical to

the success of the experiment, irrespective of whether it is on-

site or remote. These trained scientists can then return to their

laboratories and facilitate the training of group members in

the use of these systems, with the assistance of SSRL User

Support staff. A comprehensive description of the tools and

their use, along with correct sample-pin selection and

preparation, is also available through the SMB website

(http://smb.slac.stanford.edu/public/users_guide/manual/

Using_SSRL_Automated_Mounti.html).

Once screening and data collection are underway, staff are

also on hand to help with connectivity problems or beamline

troubleshooting, to give BLU-ICE or WEB-ICE help, and to

give direct experiment-related advice regarding crystal selec-

tion, data-collection strategy determination, processing soft-

ware help and data backup. Staff can contact remote scientists

by telephone, by email or using the chat feature in BLU-ICE,

and researchers can contact staff using the same methods.

SSRL User Support staff contact details are available on the

SMB website (http://smb.slac.stanford.edu/public/staff/index.

shtml).

3.2. SSRL User Guide

The SMB group website (Fig. 4; http://smb.slac.stanford.

edu) contains up-to-date information for research groups on

the state of the MX beamlines, the beamline schedule and the

SPEAR accelerator status, with links to the computing and

software resources available (through the Facilities tab),

and to the User Guide (http://smb.slac.stanford.edu/public/

users_guide/index.shtml). The User Guide is available online

to all users at any time, irrespective of whether they have

beam time, and can be downloaded as a PDF file. The guide

gives a detailed description of all aspects of MX experiments

at SSRL, from becoming an SSRL user, to detailed instruc-

tions on the use of the SAM system and the preparation of

samples, and how to use the BLU-ICE and WEB-ICE inter-

faces effectively to set up and carry out a crystal-screening and

data-collection experiment. The differences between an on-

site and a remote experiment are clearly defined, such that

novices and first-time remote-access users have all the infor-

mation at hand prior to the start of their beam time. Infor-

mation specific to the collection of MAD data and high-

resolution monochromatic data are presented, and the data-

processing software packages available to researchers are

described, along with short tutorials on the most effective use

of these programs. A set of detailed answers to frequently

asked questions (FAQs) is also included at the end of the User



electronic reprint

Guide to aid users in their experiments, and to help with

programs and with questions should they arise.

3.3. Video tutorials

The video tutorials can be accessed from the User Guide

page of the SMB website as given above, or via the link

http://smb.slac.stanford.edu/public/users_guide/tutorials/). This

project is constantly being developed and updated as new

beamline capabilities and tools become available. Current

tutorials include those that give information on tasks that can

be carried out prior to beam time, such as (i) downloading and

installing the NX client software, (ii) the best ways to fill in the

Excel spreadsheet with crystal information for a remote-access

or on-site SAM-assisted experiment, and (iii) instructions on

how to upload the completed spreadsheet to the crystal

database prior to or at the beginning of the user beam time.

Three additional videos describe (iv) the SAM-assisted

remote-access experiment in detail, demonstrating how to use

the SAM system to screen crystals in a cassette, (v) how to

interpret the screening results subsequently to select crystals

for data collection and (vi) a simulated WEB-ICE strategy

calculation. A strategy calculation for a MAD or SAD data

collection is also demonstrated.

3.4. Simulated beamlines

Prior to the start of beam time, the members of a research

group can connect to the SSRL computers and gain access to a

‘simulated’ beamline. The seven SSRL beamlines each have a

simulated counterpart which can be accessed in exactly the

same way as the ‘real’ beamlines. Access is only possible by

contacting one of the SSRL User Support staff beforehand

and asking for authorization on one of the simulated beam-

lines. Following authorization, the remote user connects to the

simulated beamline through a BLU-ICE interface indis-

tinguishable from the one that will be used later to screen

crystals and collect data. All the motors that control experi-

ment variables, such as beam size, detector distance, X-ray

energy and the beamstop position, can be moved. Since the

remote user is not actually connected to a real beamline, this

does not affect experiments currently being carried on the real

counterpart of the simulated beamline. The cassette spread-

sheet can be uploaded and new users can then be taken

through the steps involved in crystal screening by the

experienced users in the group.

The simulated beamlines are an extremely valuable

resource for a research group that may be new to remote-

access data collection, the SSRL beamlines or synchrotron

data collection in general. The best use of these simulated

beamlines involves the inclusion of a member of the SSRL

User Support staff in the remote training exercise, whereby

the use of the BLU-ICE interface on the simulated beamline

can be fully described and discussed in detail with all members

of the group. This can be facilitated by a telephone call or by

use of the desktop-sharing tools available with the NX server/

client software (http://www.nomachine.com).

3.5. Multiple NX connections

In most remote-access experiments, there are generally

several experienced people in the home

laboratory responsible for the data

collection. Because the NX client

system allows multiple connections with

the same user account, experienced

users can passively monitor the

screening and data collection being

carried out by students or postdoctoral

researchers, which still allows the

students their independence and

involvement in the decision-making

process, yet allows for the correction of

mistakes or the suggestion of alter-

native strategies. This capability also

makes it easy for SSRL User Support

staff to monitor the screening and data

collection, and to step in if they see a

potential problem. Multiple connec-

tions under the same user account can

have the name and telephone number

of the scientist associated with each one

in the Users tab of BLU-ICE, making it

easy to identify who is currently active

should User Support staff wish to

contact the researcher.

This can be extended beyond the

home laboratory to the laboratories of



Figure 4Screen capture of the SMB home page. The main tabs across the top give access to a secondary pagefor Facilities (computing, software and the remote desktop), the User Guide plus video tutorials, thebeamline schedule, forms for shipping Dewars and research-related links. The left-hand side menuchanges to list specific links as each secondary page is uploaded. Some fundamental characteristicsof the seven available beamlines are tabulated, along with quick links to commonly used web pages.

electronic reprint

collaborators, who can also connect during active beam time,

again with a name and telephone number associated with the

connection on the Users tab, either passively to monitor the

data collection, or actively to play a role in the screening,

analysis and choice of crystals, or the data collection. The

general consensus amongst SSRL research groups is that

providing beamline access to collaborators under the auspices

of their proposals has given these collaborating scientists and

their group members exposure to synchrotron beamlines that

they would never have been able to obtain without remote

access. In some cases, this exposure has led to these colla-

borating scientists writing their own successful proposals for

synchrotron beam time. A prime example of this is the beam-

time proposal submitted by the Center for Molecular Struc-

ture (CMolS) at the California State Polytechnic University

Pomona campus, which is part of the California State

University (CSU). This was not a single-user proposal, as are

the majority of proposals, but a wide-ranging one encom-



Table 2A selection of the many remote-access workshops, seminars, lectures and demonstrations facilitated or presented by SSRL scientific staff.

Type Meeting/workshop Location Date Notes

Workshop SSRL Menlo Park, California, USA October 2004 In conjunction with the Annual SSRLUsers’ Meeting


Workshop Canadian eScience Workshop Saskatoon, Saskatchewan, Canada November 2005Lecture/demonstration MBC 1 Fullerton, California, USA June 2005 Sponsored by the Center for Workshops

in Chemical SciencesSeminar ACA Annual Meeting Honolulu, Hawaii, USA July 2006Workshop HWI Buffalo, New York, USA August 2006Seminar NoBUGS 2006 Berkeley, California, USA October 2006Workshop Joint SSRL/ALS Workshop Menlo Park, California,

and Berkeley, California, USAOctober 2006 Uni-Puck and WEB-ICE

Workshop MacCHESS, Cornell Ithaca, New York, USA December 2006 Led from SSRL with participants atCHESS in a conference room

Workshop University of Melbourne Melbourne, Australia February 2007Demonstration Rotorua Proteins Meeting Rotorua, New Zealand February 2007Demonstration BSR9 Manchester, UK August 2007 Biology and Synchrotron Radiation

MeetingSeminar RAMC San Diego, California, USA September 2007 Recent Advances in Macromolecular

CrystallizationSeminar Laboratory Automation Palm Springs, California, USA January 2008Seminar CLS Saskatoon, Saskatchewan, Canada June 2008 In conjunction with the Canadian Light

Source Annual Users’ MeetingSeminar Protein Crystallography

EuropeAmsterdam, The Netherlands June 2008

Lecture/demonstration MBC 2 Fullerton, California, USA June 2008 Sponsored by the Center for Workshopsin Chemical Sciences

Lecture ACA Summer Course Indiana, Pennsylvania, USA July 2008Seminar GRC, Bates College Lewiston, Maine, USA July 2008 Diffraction Methods in Structural

Biology, Gordon Research ConferenceWorkshop CEI2008 Arlington, Virginia, USA July 2008 Cyber-Enabled Instruments 2008

Strategic Planning WorkshopWorkshop SSRL Menlo Park, California, USA October 2008 In conjunction with the Annual SSRL

Users’ MeetingWorkshop University of Pittsburgh Pittsburgh, Pennsylvania, USA October 2008 In conjunction with the Pittsburgh

Diffraction Society Annual MeetingLecture/demonstration AstraZeneca/MedImmune

Research MeetingGaithersburg, Maryland, USA February 2009

Workshop NIGMS Workshop Bethesda, Maryland, USA March 2009 Enabling Technologies for StructuralBiology

Lecture/demonstration ACA Summer Course Indiana, Pennsylvania, USA June 2009Workshop CalTech Pasadena, California, USA June 2009Seminar SRI Melbourne, Australia September 2009 10th International Conference on

Synchrotron RadiationInstrumentation

Lecture CSHL Course Cold Spring Harbor, New York, USA October 2009 Cold Spring Harbor Laboratory,X-ray Methods in Structural BiologyCourse


Seminar BSR10 Melbourne, Australia February 2010 Biology and Synchrotron RadiationMeeting

Workshop NSLS Brookhaven, New York, USA May 2010 Frontiers in Automated CrystalHandling, in conjunction with theNSLS Users’ Meeting

Lecture/demonstration ACA Summer Course Indiana, Pennsylvania, USA June 2010

electronic reprint

passing at least five CSU campuses and several different co-

PIs. The CSU campuses are traditionally undergraduate

institutions which have not typically had access to synchrotron

resources in the past, either because of a lack of funding or

because it was not something that was ever thought of as being

a possibility. Remote connection to the MX beamlines at

SSRL is now giving these researchers and their undergraduate

students continued access to state-of-the-art facilities, and is

having a positive impact on their approach to science and

research.

4. Education and outreach

4.1. Remote-access workshops

Scientific staff from the SMB group not only are regularly

involved in one-to-one user support via email and telephone

(before, during and after the experiment), but also facilitate

remote-access workshops to train new researchers in the use

of BLU-ICE and WEB-ICE, and in the practical aspects of

sample mounting and cryo-cooling, synchrotron data collec-

tion, and data processing. Several of these remote-access

workshops have been held locally at SSRL, and scientists from

the group have also traveled both nationally and inter-

nationally to hold remote-host workshops (Table 2).

The SSRL local workshops started in June 2006. They are

usually scheduled at the start of the user run, or more often,

depending on demand. Occasionally, these workshops also

take place in conjunction with the Annual SSRL Users’

Meeting (see Table 2). A typical workshop lasts half a day and

includes a thorough introduction to the experimental facilities

for MX users, including hands-on tutorials on the optimal use

of the SAM robot tools, data collection with BLU-ICE,

analysis and strategy calculations with WEB-ICE, and data

processing with the available locally installed software

packages.

The remote-host locations have included the Hauptmann–

Woodward Medical Institute (HWI) in Buffalo, New York,

USA (August 2006), the University of Melbourne, Australia

(February 2007), the University of Pittsburgh, Pennsylvania,

USA (October 2008), and the California Institute of Tech-

nology (CalTech), Pasadena, USA (June 2009). During the

University of Melbourne workshop, one of the participants

screened crystals that had previously been shipped to SSRL,

identified the best quality crystal, collected a MAD data set

and solved a novel protein structure (Schmidberger et al.,

2008), completely remotely, fully utilizing the computational

resources made available to researchers at SSRL. SSRL

remote access has also been incorporated into two workshops

sponsored by the Center for Workshops in Chemical Sciences

(http://chemistry.gsu.edu/CWCS) at CMolS, which were aimed

at faculty from predominantly undergraduate institutions.

Additional workshops at which SSRL staff have presented the

remote-access tools and capabilities are listed in Table 2.

4.2. Remote-access demonstrations, seminars and lectures

Another important method of disseminating information

regarding the SSRL remote-access tools to the user commu-

nity is through seminars and live remote-access demonstra-

tions at conferences and meetings (Table 2). This turns out to

be a perfect test of the capabilities of the NX client system,

because generally at conference locations the wireless internet

access can be somewhat intermittent and with variable speed

or bandwidth, particularly as conference participants conti-

nually connect and disconnect to the system. Since the NX

client system is designed to run on only 20 kbps of network

bandwidth, good performance is generally maintained in the

seminar locations, even on a busy wireless network. The use of

a remote-access connection to either an SSRL MX beamline

or a simulated beamline, when combined with conference

lectures or seminars, workshop presentations, or in a formal

university teaching environment, is a powerful pedagogical

tool. We strongly encourage and support such use of the SSRL

systems by the scientific community.

5. Conclusions

The SAM system has been used to screen a total of over

300 000 crystals for diffraction quality in the past seven years,

and has most certainly proved its worth. When coupled with

the remote-access capabilities that have been available to

scientific user groups (general users) for the past five years,

this system has led to the MX beamlines at SSRL becoming a

true high-throughput facility. The efficiency of the research

groups who use remote access has increased remarkably,

which has in turn given synchrotron access to more user

groups than ever before and resulted in a surge in the number

of user starts at SSRL. Researchers are now easily able to

screen all crystals being grown in the laboratory, in order to

choose the best possible crystals for data collection, whereas

before they may have limited themselves to the crystals that

simply appeared to be the best, or else spent innumerable

hours on a home source screening crystals. It has become

increasing clear that many user groups are forgoing in-house

screening, and simply cryo-cooling as many crystals as they

can fit into a cassette or Uni-pucks and letting the robust

efficient SAM system do the work for them. This is exactly the

vision the developers of the Stanford auto-mounter had in

mind for the system: to provide a true high-throughput plat-

form for the screening of large numbers of protein crystals.

The ways in which remote access to the SSRL beamlines

can facilitate training and collaboration have most certainly

not gone unnoticed by the scientific community. All research

groups who collect their data remotely use the available tools

provided by SSRL to train and educate their laboratory

members in the most effective ways to collect the best possible

diffraction data. Approximately 60% of researchers with

active proposals and current beam time have at some point

had collaborators participate in remote-access data collection,

where they take either a passive or an active role, and in some

cases have even used the time to train or educate members of

their own laboratory. The way in which remote access to SSRL

beamlines serves to bring collaborators together is one of the

most fundamental examples of what has been described as a

‘cultural community’, as noted by the Director of the NSF


J. Appl. Cryst. (2010). 43, 1261–1270 Clyde A. Smith et al. � Remote access to SSRL beamlines 1269electronic reprint

report Cyberinfrastructure Vision for 21st Century Discovery

(NSF Cyberinfrastructure Council, 2007). This idea is some-

thing that we at SSRL will continue to foster and promote. At

SSRL we are dedicated to making the remote-access experi-

ence as easy, efficient and instructive as possible, and making a

synchrotron beamline accessible to anyone in the scientific

community who has a need for a high-intensity X-ray beam

and expects high-quality diffraction data.

The authors acknowledge the entire SAM and remote-

access development teams, which include members of the

Joint Center for Structural Genomics and the SSRL Structural

Molecular Biology group. Special thanks are extended to Lisa

Dunn for help with analysis of the user statistics. Operations

funding for the Stanford Synchrotron Radiation Lightsource is

provided by the US Department of Energy Office of Basic

Energy Sciences. The SSRL Structural Molecular Biology

Program is supported by the Biomedical Technology Program

of the National Center for Research Resources of the US

National Institutes of Health, by the US Department of

Energy Office of Biological and Environmental Research, and

by the National Institute of General Medical Sciences of the

US National Institutes of Health. We also thank Katherine

Kantardjieff at CMolS, Eddie Snell at HWI, Peter Turner at

the University of Sydney, Guillermo Calero and JoAnne Yeh

at the University of Pittsburgh, and Doug Rees at CalTech for

organizing and facilitating remote-access workshops.

References

Burley, S. K., Joachimiak, A., Montelione, G. T. & Wilson, I. A.(2008). Structure, 16, 5–11.

Cipriani, F. et al. (2006). Acta Cryst. D62, 1251–1259.Cohen, A. E., Ellis, P. J., Miller, M. D., Deacon, A. M. & Phizackerley,

R. P. (2002). J. Appl. Cryst. 35, 720–726.Doniach, S., Hodgson, K., Lindau, I., Pianetta, P. & Winick, H. (1997).J. Synchrotron Rad. 4, 380–395.

Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126–2132.Gonzalez, A., Moorhead, P., McPhillips, S. E., Song, J., Sharp, K.,

Taylor, J. R., Adams, P. D., Sauter, N. K. & Soltis, S. M. (2008). J.Appl. Cryst. 41, 176–184.

Karain, W. I., Bourenkov, G. P., Blume, H. & Bartunik, H. D. (2002).Acta Cryst. D58, 1519–1522.

Kincaid, B. M., Eisenberger, P., Hodgson, K. O. & Doniach, S. (1975).Proc. Natl Acad. Sci. USA, 72, 2340–2342.

Lesley, S. A. et al. (2002). Proc. Natl Acad. Sci. USA, 99, 11664–11669.Leslie, A. G. W. (1992). In Joint CCP4/ESF-EACMB Newsletter onProtein Crystallography, Vol. 26. Warrington: Daresbury Labora-tory.

McPhillips, T. M., McPhillips, S. E., Chiu, H.-J., Cohen, A. E., Deacon,A. M., Ellis, P. J., Garman, E., Gonzalez, A., Sauter, N. K.,Phizackerley, R. P., Soltis, S. M. & Kuhn, P. (2002). J. SynchrotronRad. 9, 401–406.

Muchmore, S. W., Olson, J., Jones, R., Pan, J., Blum, M., Greer, J.,Merrick, S. M., Magdalinos, P. & Nienaber, V. L. (2000). Struct.Folding Des. 8, R243–R246.

NSF Cyberinfrastructure Council (2007). Cyberinfrastructure Visionfor 21st Century Discovery. National Science Foundation,Arlington, Virginia, USA. http://www.nsf.gov/pubs/2007/nsf0728/nsf0728.pdf.

Ohana, J., Jacquamet, L., Joly, J., Bertoni, A., Taunier, P., Michel, L.,Charrault, P., Pirocchi, M., Carpentier, P., Borel, F., Kahn, R. &Ferrer, J.-L. (2004). J. Appl. Cryst. 37, 72–77.

Parkin, S. & Hope, H. (1998). J. Appl. Cryst. 31, 945–953.Pflugrath, J. W. (2004). Methods Enzymol. 34, 415–423.Phillips, J. C. & Hodgson, K. O. (1980). Acta Cryst. A36, 856–864.Phillips, J. C., Templeton, D. H., Templeton, L. K. & Hodgson, K. O.

(1978). Science, 201, 257–259.Phillips, J. C., Wlodawer, A., Goodfellow, J. M., Watenpaugh, K. D.,

Sieker, L. C., Jensen, L. H. & Hodgson, K. O. (1977). Acta Cryst.A33, 445–455.

Phillips, J. C., Wlodawer, A., Yevitz, M. M. & Hodgson, K. O. (1976).Proc. Natl Acad. Sci. USA, 73, 128–132.

Pohl, E., Ristau, U., Gehrmann, T., Jahn, D., Robrahn, B., Malthan,D., Dobler, H. & Hermes, C. (2004). J. Synchrotron Rad. 11, 372–377.

Robinson, H., Soares, A. S., Becker, M., Sweet, R. & Heroux, A.(2006). Acta Cryst. D62, 1336–1339.

Rodgers, D. W. (2001). International Tables for Crystallography,Vol. F, Crystallography of Biological Macromolecules, edited by M.Rossman & E. Arnold, pp. 202–208. Dordrecht: Kluwer AcademicPublishers.

Schmidberger, J. W., Wilce, J. A., Weightman, A. J., Whisstock, J. C. &Wilce, M. C. (2008). J. Mol. Biol. 378, 284–294.

Smith, C. A. & Cohen, A. E. (2008). J. Assoc. Lab. Autom. 13, 335–343.

Snell, G., Cork, C., Nordmeyer, R., Cornell, E., Meigs, G., Yegian, D.,Jaklevic, J., Jin, J., Stevens, R. C. & Earnest, T. (2004). Structure, 12,537–545.

Soltis, S. M. et al. (2008). Acta Cryst. D64, 1210–1221.Templeton, D. H., Templeton, L. K., Phillips, J. C. & Hodgson, K. O.

(1980). Acta Cryst. A36, 436–442.Ueno, G., Hirose, R., Ida, K., Kumasaka, T. & Yamamoto, M. (2004).J. Appl. Cryst. 37, 867–873.

Warren, J. E., Diakun, G., Bushnell-Wye, G., Fisher, S., Thalal, A.,Helliwell, M. & Helliwell, J. R. (2008). J. Synchrotron Rad. 15, 191–194.



electronic reprint

Documents

Remote access to crystallography beamlines at SSRL: novel tools